Inflammatory monocytes promote granuloma control of Yersinia infection
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE194334 | GEO | 2022/02/07
REPOSITORIES: GEO
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Project description:The Golgi stress response is a homeostatic mechanism that augments the functional capacity of the Golgi apparatus when Golgi function becomes insufficient (Golgi stress). Three response pathways of the Golgi stress response have been identified in mammalian cells, the TFE3, HSP47 and CREB3 pathways, which augment the capacity of specific Golgi functions such as N-glycosylation, anti-apoptotic activity and pro-apoptotic activity, respectively. On the contrary, glycosylation of proteoglycans (PGs) is another important function of the Golgi, although the response pathway upregulating expression of glycosylation enzymes for PGs in response to Golgi stress remains unknown. Here, we found that expression of glycosylation enzymes for PGs was induced upon insufficiency of PG glycosylation capacity in the Golgi (PG-Golgi stress), and that transcriptional induction of genes encoding glycosylation enzymes for PGs was independent of the known Golgi stress response pathways and ER stress response. Promoter analyses of genes encoding these glycosylation enzymes revealed the novel enhancer element PGSE, which regulates their transcriptional induction upon PG-Golgi stress. From these observations, the response pathway we discovered is a novel Golgi stress response pathway, which we have named the PG pathway.
2018-09-14 | GSE119909 | GEO
Project description:The Golgi stress response is a homeostatic mechanism that augments the functional capacity of the Golgi apparatus when Golgi function becomes insufficient (Golgi stress). Three response pathways of the Golgi stress response have been identified in mammalian cells, the TFE3, HSP47 and CREB3 pathways, which augment the capacity of specific Golgi functions such as N-glycosylation, anti-apoptotic activity and pro-apoptotic activity, respectively. On the contrary, glycosylation of proteoglycans (PGs) is another important function of the Golgi, although the response pathway upregulating expression of glycosylation enzymes for PGs in response to Golgi stress remains unknown. Here, we found that expression of glycosylation enzymes for PGs was induced upon insufficiency of PG glycosylation capacity in the Golgi (PG-Golgi stress), and that transcriptional induction of genes encoding glycosylation enzymes for PGs was independent of the known Golgi stress response pathways and ER stress response. Promoter analyses of genes encoding these glycosylation enzymes revealed the novel enhancer element PGSE, which regulates their transcriptional induction upon PG-Golgi stress. From these observations, the response pathway we discovered is a novel Golgi stress response pathway, which we have named the PG pathway.
2018-08-01 | GSE117938 | GEO
Project description:Plants possess various defense strategies to counter attacks from microorganisms or herbivores. For example, plants reduce the cell-wall-macerating activity of pathogen- or insect-derived polygalacturonases (PGs) by expressing PG-inhibiting proteins (PGIPs). PGs and PGIPs belong to multi-gene families believed to have been shaped by an evolutionary arms race. The mustard leaf beetle Phaedon cochleariae expresses both active PGs and catalytically inactive PG pseudoenzymes. Previous studies demonstrated that (i) PGIPs target beetle PGs and (ii) the role of PG pseudoenzymes remains elusive, despite having been linked to the pectin degradation pathway. For further insight into the interaction between plant PGIPs and beetle PG family members, we combined affinity purification with proteomics and gene expression analyses, and identified novel inhibitors of beetle PGs from Chinese cabbage (Brassica rapa ssp. pekinensis). A beetle PG pseudoenzyme was not targeted by PGIPs, but instead interacted with PGIP-like proteins. Phylogenetic analysis revealed that PGIP-like proteins clustered apart from classical PGIPs but together with proteins, which have been involved in developmental processes. Our results indicate that PGIP-like proteins represent not only interesting novel PG inhibitor candidates in addition to classical PGIPs, but also fascinating new players in the arms race between herbivorous beetles and plant defenses.
2021-06-07 | PXD022562 | Pride
Project description:In the effort to identify novel, relevant prognostic factors for the clinical monitoring of patients affected by squamous cell carcinomas of the oral cavity (SCCOC) we have pursued a molecular screening at the gene and protein level on 166 surgical specimens derived from patients with an accessible clinical history and >2 years follow-up. The screening was focalized on cell surface proteoglycans (PGs) based upon the assumption that altered expression of individual or groups of PGs may predict disease course and therapeutic response, and thereby allow for a clusterization of patients in discrete subsets. The 11 PGs contemplated in the screening and including syndecan-1-4 (SDC1-SDC4), glypican-1-6 (GPC1-GPC6) and NG2, were found to be transcribed at variable levels and with a decreasing frequencies SDC1>SDC4>SDC2>SDC3>GPC4>GPC3>GPC1 >GPC5>CSPG4>GPC6>GPC2. SCCOC cells de novo transcribed GPC2, GPC5 and NG2 and regulated all SDCs, GPC1, -3, -4 and -6, suggesting that an altered surface profile of PG is a characterizing trait of these tumor cells In situ distributional analysis of these PGs on a total of 149 cases revealed many fewer lesions actually translated the molecules which were detected with a frequency range of 14% (SDC2) to 92% (SDC1). Noteworthy was, however, that SDC2 was present in the intra-lesional stroma and in association with neovessels in all the cases, suggesting that this specific PG was a key element of stromal fibroblasts and angiogenic structures. Poor translational efficacy of several of the PGs was accompanied by an apparent retention of the molecules within the cytoplasm of SCCOC cells. This finding suggest that modulated expression of cell surface PGs may be a representative secondary event in SCCOC and that these carcinoma cells do not mount up an effective intracellular machinery for proper shuttling and membrane incorporation of the PGs.
2013-11-01 | GSE33788 | GEO
Project description:Bufotoxin is an endogenous toxin made up of several physiologically active components that toads deploy as a defense against their natural enemies. Bufadienolides (BDS), which is isolated from bufotoxin, is an important anticancer drug, and other components such as bufotenine and alkaloids are also important drug resources. The distribution characteristics and biosynthesis of bufotoxins in the postauricular glands (PGs) of toads are not well understood. We examined the toad's PGs using the MADLI/MSI technique, a total of 1,872 components were found, and some pharmacological components were visible. These findings indicate that bufotoxins are primarily abundant in the plasma glands (pG) and epidermal tissues of the glands. By using single-cell sequencing, it was possible to create a single-cell atlas of 9316 PGs cells. These cells were then categorized into nine clusters using marker genes, and two types of epithelial cells were verified using in situ hybridization investigations. It was confirmed that cholesterol is a precursor component of BDS biosynthesis, we concentrated on the cholesterol metabolism component and postulated the primary bile acid pathway as a downstream biosynthesis pathway of BDS through transcriptomic studies of two pG and mucous glands (MG) with distinct secretory functions. Optimal and silenced genes for potential BDS synthesis pathways, toad toxin tryptamine and alkaloid biosynthesis, terpene skeleton and steroid hormones were identified by calculating the cellular coverage of genes. Our data demonstrate the metabolic mapping of bufotoxins in the PGs of the toad, and create the first single-cell atlas of PGs in the toad, providing a reference for the study of biosynthesis of natural active ingredients in animals.
2024-11-05 | PXD057113 | Pride
Project description:In the effort to identify novel, relevant prognostic factors for the clinical monitoring of patients affected by squamous cell carcinomas of the oral cavity (SCCOC) we have pursued a molecular screening at the gene and protein level on 166 surgical specimens derived from patients with an accessible clinical history and >2 years follow-up. The screening was focalized on cell surface proteoglycans (PGs) based upon the assumption that altered expression of individual or groups of PGs may predict disease course and therapeutic response, and thereby allow for a clusterization of patients in discrete subsets. The 11 PGs contemplated in the screening and including syndecan-1-4 (SDC1-SDC4), glypican-1-6 (GPC1-GPC6) and NG2, were found to be transcribed at variable levels and with a decreasing frequencies SDC1>SDC4>SDC2>SDC3>GPC4>GPC3>GPC1 >GPC5>CSPG4>GPC6>GPC2. SCCOC cells de novo transcribed GPC2, GPC5 and NG2 and regulated all SDCs, GPC1, -3, -4 and -6, suggesting that an altered surface profile of PG is a characterizing trait of these tumor cells In situ distributional analysis of these PGs on a total of 149 cases revealed many fewer lesions actually translated the molecules which were detected with a frequency range of 14% (SDC2) to 92% (SDC1). Noteworthy was, however, that SDC2 was present in the intra-lesional stroma and in association with neovessels in all the cases, suggesting that this specific PG was a key element of stromal fibroblasts and angiogenic structures. Poor translational efficacy of several of the PGs was accompanied by an apparent retention of the molecules within the cytoplasm of SCCOC cells. This finding suggest that modulated expression of cell surface PGs may be a representative secondary event in SCCOC and that these carcinoma cells do not mount up an effective intracellular machinery for proper shuttling and membrane incorporation of the PGs. A total of 166 surgical specimens of primary SCCOC were collected after informed consent from individuals who underwent surgical removal of the tumor lesions and RNA from 119 surgical specimens were extracted; a pool of RNAs extracted from 5 normal epithelia tissues was adopted as a sample calibrator (HEALTHY sample). cDNA from each samples and from pool of normal epithelial were loaded on TLDA and amplified. HEALTHY sample were amplified 20 times in two replicates (in each TLDA card); each patient sample were amplified 1 time in two replicates and 7 samples of them were loaded two times in a separate TLDA card (for a total of 4 replicates).
2013-11-01 | E-GEOD-33788 | biostudies-arrayexpress
Project description:This is part of a cross-species approach to characterize transcriptional response of the insect prothoracic gland (PG) to the prothoracicotropic hormone (PTTH). Genome-wide response of the PG to PTTH was analyzed in vitro in Bombyx and in vivo in Drosophila, and the results were compared to identify common components in the PTTH signaling pathway. Bombyx PGs were incubated in vitro for 1 or 3 hours with or without 10 nM recombinant PTTH. 12-18 larvae were used to prepare each RNA sample, and the experiment was conducted twice. Total RNA samples from two independent preparations were combined to obtain a single RNA sample for each treatment, which was subjected to RNA-seq.
2016-07-29 | E-GEOD-84963 | biostudies-arrayexpress
Project description:We report the open chromatin landscape in primary human macrophages and foam cells using FAIRE-seq CD14+ monocytes were isolated from the blood of 3 healthy volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stimulating factor and then treated for 48 hours with either oxidized low density lipoprotein (oxLDL) to induce foam cell formation or with a control buffer that lacked oxLDL. The resulting six samples were then subjected to FAIRE-seq using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67).
2015-04-08 | E-GEOD-54971 | biostudies-arrayexpress
Project description:Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathwaysin these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor.
2024-09-28 | GSE242272 | GEO
Project description:Prostaglandins (PGs) are inflammatory mediators. Aspirin-like non-steroidal anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX), an initiating enzyme of PG biosynthesis1. Daily use of aspirin-like drugs lowers the risk of cancer death not only prophylactically but therapeutically suggesting critical roles of PGs in cancer. However, general mechanisms by which PGs contribute to progression of a wide variety of human cancers remain elusive. Here, using scRNAseq analysis comparing immune cells infiltrating human tumors and a syngeneic mouse tumor, we have dissected this issue. We found that in human tumors, COX is dominantly expressed in infiltrating myeloid cells, and, among PG receptors, PGE receptor EP4 and to a less extent EP2 are expressed in both T cells and myeloid cells. DEG analysis between PTGER4hi and PTGER4lo CD8+ T cells indicates downregulation of IL-2-STAT5 signaling, oxidative phosphorylation, glycolysis and Myc targets in EP4hi CD8+ T cells, as revealed by suppressed expression of IL-2 receptor subunit gene and genes of OXPHOS, glycolytic enzymes and ribosomal proteins (RPs). Similar downregulation of OXPHOS, glycolytic enzymes and RP genes is found in PTGER4hi myeloid cells. Notably, such downregulation of OXPHOS and RP genes was found in immune cells infiltrating LLC1 mouse tumor, and reversed by treatment of tumor-bearing mice with EP2 and EP4 antagonists. In vitro in CD8+ T cells, EP4 is induced upon TCR activation and PGE2 acts on EP4, downregulates Il2ra expression and suppresses expression of Myc and PGC-1, thereby impairing both mitochondria and glycolysis as well as ribosome biogenesis in these cells. Similarly, EP4 is induced upon activation in macrophages and PGE2 downregulates Myc and OXPHOS pathwaysin these cells irrespective of other stimuli. These results demonstrate that PGE2 shapes immunosuppressive tumor microenvironment by hampering bioenergetic metabolism and ribosome biogenesis in infiltrating immune cells via EP4 receptor.
2024-09-28 | GSE242271 | GEO